HEADER HYDROLASE 18-AUG-16 5LR0 TITLE BINDING DOMAIN OF BOTULINUM NEUROTOXIN DC IN COMPLEX WITH SIALYLT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BOTULINUM NEUROTOXIN D/C PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: D/C MOSAIC NEUROTOXIN,NEUROTOXIN,NEUROTOXIN TYPE DC; COMPND 5 EC: 3.4.24.69; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM BOTULINUM; SOURCE 3 ORGANISM_TAXID: 1491; SOURCE 4 GENE: BONT, BONT D, C, DC, NT; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BOTULNIMUN NEUROTOXIN, CARBOHYDRATE BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.P.-A.BERNTSSON,P.STENMARK REVDAT 4 10-JAN-24 5LR0 1 HETSYN LINK REVDAT 3 29-JUL-20 5LR0 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 06-DEC-17 5LR0 1 JRNL REVDAT 1 30-AUG-17 5LR0 0 JRNL AUTH S.ZHANG,R.P.BERNTSSON,W.H.TEPP,L.TAO,E.A.JOHNSON,P.STENMARK, JRNL AUTH 2 M.DONG JRNL TITL STRUCTURAL BASIS FOR THE UNIQUE GANGLIOSIDE AND CELL JRNL TITL 2 MEMBRANE RECOGNITION MECHANISM OF BOTULINUM NEUROTOXIN DC. JRNL REF NAT COMMUN V. 8 1637 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29158482 JRNL DOI 10.1038/S41467-017-01534-Z REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 38598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2032 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2484 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6709 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.03000 REMARK 3 B22 (A**2) : -2.03000 REMARK 3 B33 (A**2) : 4.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.438 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.258 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.202 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.842 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6956 ; 0.006 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 6470 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9413 ; 1.175 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14845 ; 0.921 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 813 ; 6.313 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 351 ;38.694 ;24.929 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1206 ;13.811 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.922 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1029 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7860 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1716 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3270 ; 1.622 ; 4.018 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3269 ; 1.622 ; 4.018 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4077 ; 2.867 ; 6.011 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 864 1284 B 864 1284 22871 0.110 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5LR0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98405 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40710 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 48.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : 0.23900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : 1.43700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4ISQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM NITRATE, 20% PEG 3350, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 105.23050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 54.84950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.84950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.61525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.84950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.84950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 157.84575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.84950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.84950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.61525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.84950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.84950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 157.84575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 105.23050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 854 REMARK 465 HIS A 855 REMARK 465 HIS A 856 REMARK 465 HIS A 857 REMARK 465 HIS A 858 REMARK 465 HIS A 859 REMARK 465 HIS A 860 REMARK 465 TYR A 861 REMARK 465 PHE A 862 REMARK 465 SER A 863 REMARK 465 ASN A 924 REMARK 465 ILE A 925 REMARK 465 VAL A 926 REMARK 465 THR A 1034 REMARK 465 GLY A 1035 REMARK 465 ASN A 1051 REMARK 465 THR A 1052 REMARK 465 GLY A 1053 REMARK 465 LEU A 1054 REMARK 465 ILE A 1055 REMARK 465 THR A 1056 REMARK 465 SER A 1057 REMARK 465 ASP A 1058 REMARK 465 SER A 1059 REMARK 465 MET B 854 REMARK 465 HIS B 855 REMARK 465 HIS B 856 REMARK 465 HIS B 857 REMARK 465 HIS B 858 REMARK 465 HIS B 859 REMARK 465 HIS B 860 REMARK 465 TYR B 861 REMARK 465 PHE B 862 REMARK 465 PRO B 1050 REMARK 465 ASN B 1051 REMARK 465 THR B 1052 REMARK 465 GLY B 1053 REMARK 465 LEU B 1054 REMARK 465 ILE B 1055 REMARK 465 THR B 1056 REMARK 465 SER B 1057 REMARK 465 ASP B 1058 REMARK 465 SER B 1059 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O3 GAL D 2 C2 SIA B 1301 0.98 REMARK 500 O3 NGA D 1 O5 GAL D 2 1.91 REMARK 500 O3 GAL D 2 O6 SIA B 1301 1.93 REMARK 500 O3 GAL D 2 C3 SIA B 1301 1.94 REMARK 500 C3 GAL D 2 C2 SIA B 1301 2.05 REMARK 500 NH1 ARG B 914 OD1 ASN B 1047 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 913 40.73 -84.74 REMARK 500 MET A 930 72.79 -110.29 REMARK 500 SER A 970 -130.46 47.39 REMARK 500 GLU A 984 129.24 -172.93 REMARK 500 ASN A 996 51.59 -143.92 REMARK 500 ALA A1073 32.68 -87.16 REMARK 500 ASN A1139 29.77 -149.58 REMARK 500 ASN A1172 -1.76 67.74 REMARK 500 SER A1239 -163.57 -125.13 REMARK 500 TYR A1251 -61.52 -138.89 REMARK 500 GLU A1265 -69.06 64.23 REMARK 500 ASN B 865 58.29 -100.39 REMARK 500 ASP B 913 33.56 -81.49 REMARK 500 GLU B 923 31.15 -88.62 REMARK 500 GLU B 932 -83.19 -106.68 REMARK 500 SER B 970 -128.47 47.98 REMARK 500 ASN B 996 49.38 -141.31 REMARK 500 ALA B1073 34.74 -87.42 REMARK 500 ASN B1139 32.50 -150.54 REMARK 500 GLU B1161 -4.30 72.95 REMARK 500 ASN B1172 -2.38 67.45 REMARK 500 CYS B1214 87.23 -150.87 REMARK 500 SER B1239 -159.08 -122.40 REMARK 500 PHE B1245 -166.91 -160.12 REMARK 500 TYR B1251 -67.21 -133.03 REMARK 500 GLU B1265 -63.09 64.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN B 1154 ASP B 1155 -147.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SIA B 1301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ISR RELATED DB: PDB REMARK 900 4ISR CONTAINS THE SAME PROTEIN COMPLEXED WITH RAT SYNAPTOTAGMIN I REMARK 900 PEPTIDE REMARK 900 RELATED ID: 4ISQ RELATED DB: PDB REMARK 900 4ISQ CONTAINS THE SAME PROTEIN COMPLEXED WITH HUMAN SYNAPTOTAGMIN I REMARK 900 PEPTIDE DBREF 5LR0 A 863 1284 UNP A5JGM8 A5JGM8_CLOBO 863 1284 DBREF 5LR0 B 863 1284 UNP A5JGM8 A5JGM8_CLOBO 863 1284 SEQADV 5LR0 MET A 854 UNP A5JGM8 INITIATING METHIONINE SEQADV 5LR0 HIS A 855 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS A 856 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS A 857 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS A 858 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS A 859 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS A 860 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 TYR A 861 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 PHE A 862 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 MET B 854 UNP A5JGM8 INITIATING METHIONINE SEQADV 5LR0 HIS B 855 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS B 856 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS B 857 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS B 858 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS B 859 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 HIS B 860 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 TYR B 861 UNP A5JGM8 EXPRESSION TAG SEQADV 5LR0 PHE B 862 UNP A5JGM8 EXPRESSION TAG SEQRES 1 A 431 MET HIS HIS HIS HIS HIS HIS TYR PHE SER ILE ASN ASP SEQRES 2 A 431 SER LYS ILE LEU SER LEU GLN ASN LYS LYS ASN THR LEU SEQRES 3 A 431 MET ASP THR SER GLY TYR ASN ALA GLU VAL ARG VAL GLU SEQRES 4 A 431 GLY ASN VAL GLN LEU ASN PRO ILE PHE PRO PHE ASP PHE SEQRES 5 A 431 LYS LEU GLY SER SER GLY ASP ASP ARG GLY LYS VAL ILE SEQRES 6 A 431 VAL THR GLN ASN GLU ASN ILE VAL TYR ASN ALA MET TYR SEQRES 7 A 431 GLU SER PHE SER ILE SER PHE TRP ILE ARG ILE ASN LYS SEQRES 8 A 431 TRP VAL SER ASN LEU PRO GLY TYR THR ILE ILE ASP SER SEQRES 9 A 431 VAL LYS ASN ASN SER GLY TRP SER ILE GLY ILE ILE SER SEQRES 10 A 431 ASN PHE LEU VAL PHE THR LEU LYS GLN ASN GLU ASN SER SEQRES 11 A 431 GLU GLN ASP ILE ASN PHE SER TYR ASP ILE SER LYS ASN SEQRES 12 A 431 ALA ALA GLY TYR ASN LYS TRP PHE PHE VAL THR ILE THR SEQRES 13 A 431 THR ASN MET MET GLY ASN MET MET ILE TYR ILE ASN GLY SEQRES 14 A 431 LYS LEU ILE ASP THR ILE LYS VAL LYS GLU LEU THR GLY SEQRES 15 A 431 ILE ASN PHE SER LYS THR ILE THR PHE GLN MET ASN LYS SEQRES 16 A 431 ILE PRO ASN THR GLY LEU ILE THR SER ASP SER ASP ASN SEQRES 17 A 431 ILE ASN MET TRP ILE ARG ASP PHE TYR ILE PHE ALA LYS SEQRES 18 A 431 GLU LEU ASP ASP LYS ASP ILE ASN ILE LEU PHE ASN SER SEQRES 19 A 431 LEU GLN TYR THR ASN VAL VAL LYS ASP TYR TRP GLY ASN SEQRES 20 A 431 ASP LEU ARG TYR ASP LYS GLU TYR TYR MET ILE ASN VAL SEQRES 21 A 431 ASN TYR MET ASN ARG TYR MET SER LYS LYS GLY ASN GLY SEQRES 22 A 431 ILE VAL PHE ASN THR ARG LYS ASN ASN ASN ASP PHE ASN SEQRES 23 A 431 GLU GLY TYR LYS ILE ILE ILE LYS ARG ILE ARG GLY ASN SEQRES 24 A 431 THR ASN ASP THR ARG VAL ARG GLY GLU ASN VAL LEU TYR SEQRES 25 A 431 PHE ASN THR THR ILE ASP ASN LYS GLN TYR SER LEU GLY SEQRES 26 A 431 MET TYR LYS PRO SER ARG ASN LEU GLY THR ASP LEU VAL SEQRES 27 A 431 PRO LEU GLY ALA LEU ASP GLN PRO MET ASP GLU ILE ARG SEQRES 28 A 431 LYS TYR GLY SER PHE ILE ILE GLN PRO CYS ASN THR PHE SEQRES 29 A 431 ASP TYR TYR ALA SER GLN LEU PHE LEU SER SER ASN ALA SEQRES 30 A 431 THR THR ASN ARG LEU GLY ILE LEU SER ILE GLY SER TYR SEQRES 31 A 431 SER PHE LYS LEU GLY ASP ASP TYR TRP PHE ASN HIS GLU SEQRES 32 A 431 TYR LEU ILE PRO VAL ILE LYS ILE GLU HIS TYR ALA SER SEQRES 33 A 431 LEU LEU GLU SER THR SER THR HIS TRP VAL PHE VAL PRO SEQRES 34 A 431 ALA SER SEQRES 1 B 431 MET HIS HIS HIS HIS HIS HIS TYR PHE SER ILE ASN ASP SEQRES 2 B 431 SER LYS ILE LEU SER LEU GLN ASN LYS LYS ASN THR LEU SEQRES 3 B 431 MET ASP THR SER GLY TYR ASN ALA GLU VAL ARG VAL GLU SEQRES 4 B 431 GLY ASN VAL GLN LEU ASN PRO ILE PHE PRO PHE ASP PHE SEQRES 5 B 431 LYS LEU GLY SER SER GLY ASP ASP ARG GLY LYS VAL ILE SEQRES 6 B 431 VAL THR GLN ASN GLU ASN ILE VAL TYR ASN ALA MET TYR SEQRES 7 B 431 GLU SER PHE SER ILE SER PHE TRP ILE ARG ILE ASN LYS SEQRES 8 B 431 TRP VAL SER ASN LEU PRO GLY TYR THR ILE ILE ASP SER SEQRES 9 B 431 VAL LYS ASN ASN SER GLY TRP SER ILE GLY ILE ILE SER SEQRES 10 B 431 ASN PHE LEU VAL PHE THR LEU LYS GLN ASN GLU ASN SER SEQRES 11 B 431 GLU GLN ASP ILE ASN PHE SER TYR ASP ILE SER LYS ASN SEQRES 12 B 431 ALA ALA GLY TYR ASN LYS TRP PHE PHE VAL THR ILE THR SEQRES 13 B 431 THR ASN MET MET GLY ASN MET MET ILE TYR ILE ASN GLY SEQRES 14 B 431 LYS LEU ILE ASP THR ILE LYS VAL LYS GLU LEU THR GLY SEQRES 15 B 431 ILE ASN PHE SER LYS THR ILE THR PHE GLN MET ASN LYS SEQRES 16 B 431 ILE PRO ASN THR GLY LEU ILE THR SER ASP SER ASP ASN SEQRES 17 B 431 ILE ASN MET TRP ILE ARG ASP PHE TYR ILE PHE ALA LYS SEQRES 18 B 431 GLU LEU ASP ASP LYS ASP ILE ASN ILE LEU PHE ASN SER SEQRES 19 B 431 LEU GLN TYR THR ASN VAL VAL LYS ASP TYR TRP GLY ASN SEQRES 20 B 431 ASP LEU ARG TYR ASP LYS GLU TYR TYR MET ILE ASN VAL SEQRES 21 B 431 ASN TYR MET ASN ARG TYR MET SER LYS LYS GLY ASN GLY SEQRES 22 B 431 ILE VAL PHE ASN THR ARG LYS ASN ASN ASN ASP PHE ASN SEQRES 23 B 431 GLU GLY TYR LYS ILE ILE ILE LYS ARG ILE ARG GLY ASN SEQRES 24 B 431 THR ASN ASP THR ARG VAL ARG GLY GLU ASN VAL LEU TYR SEQRES 25 B 431 PHE ASN THR THR ILE ASP ASN LYS GLN TYR SER LEU GLY SEQRES 26 B 431 MET TYR LYS PRO SER ARG ASN LEU GLY THR ASP LEU VAL SEQRES 27 B 431 PRO LEU GLY ALA LEU ASP GLN PRO MET ASP GLU ILE ARG SEQRES 28 B 431 LYS TYR GLY SER PHE ILE ILE GLN PRO CYS ASN THR PHE SEQRES 29 B 431 ASP TYR TYR ALA SER GLN LEU PHE LEU SER SER ASN ALA SEQRES 30 B 431 THR THR ASN ARG LEU GLY ILE LEU SER ILE GLY SER TYR SEQRES 31 B 431 SER PHE LYS LEU GLY ASP ASP TYR TRP PHE ASN HIS GLU SEQRES 32 B 431 TYR LEU ILE PRO VAL ILE LYS ILE GLU HIS TYR ALA SER SEQRES 33 B 431 LEU LEU GLU SER THR SER THR HIS TRP VAL PHE VAL PRO SEQRES 34 B 431 ALA SER HET NGA C 1 15 HET GAL C 2 11 HET SIA C 3 20 HET NGA D 1 15 HET GAL D 2 11 HET SIA B1301 20 HETNAM NGA 2-ACETAMIDO-2-DEOXY-BETA-D-GALACTOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETSYN NGA N-ACETYL-BETA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NGA BETA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 NGA ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-D-GALACTOSAMINE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID FORMUL 3 NGA 2(C8 H15 N O6) FORMUL 3 GAL 2(C6 H12 O6) FORMUL 3 SIA 2(C11 H19 N O9) FORMUL 6 HOH *143(H2 O) HELIX 1 AA1 ILE A 864 ASP A 866 5 3 HELIX 2 AA2 ASP A 992 ASN A 996 5 5 HELIX 3 AA3 ASP A 1077 LEU A 1088 1 12 HELIX 4 AA4 ASN A 1114 MET A 1116 5 3 HELIX 5 AA5 PRO A 1199 GLY A 1207 1 9 HELIX 6 AA6 TYR A 1267 LEU A 1271 5 5 HELIX 7 AA7 SER A 1273 THR A 1276 5 4 HELIX 8 AA8 ASN B 924 TYR B 931 5 8 HELIX 9 AA9 ASP B 992 ASN B 996 5 5 HELIX 10 AB1 ASP B 1077 LEU B 1088 1 12 HELIX 11 AB2 ASN B 1114 MET B 1116 5 3 HELIX 12 AB3 PRO B 1199 GLY B 1207 1 9 HELIX 13 AB4 TYR B 1267 LEU B 1271 5 5 HELIX 14 AB5 SER B 1273 THR B 1276 5 4 SHEET 1 AA1 5 LEU A 879 ASP A 881 0 SHEET 2 AA1 5 LYS A 868 ASN A 874 -1 N GLN A 873 O MET A 880 SHEET 3 AA1 5 ASN A1063 PHE A1072 -1 O PHE A1069 N LEU A 872 SHEET 4 AA1 5 PHE A 905 GLY A 908 -1 N LEU A 907 O MET A1064 SHEET 5 AA1 5 GLN A 896 LEU A 897 -1 N GLN A 896 O LYS A 906 SHEET 1 AA2 7 LEU A 879 ASP A 881 0 SHEET 2 AA2 7 LYS A 868 ASN A 874 -1 N GLN A 873 O MET A 880 SHEET 3 AA2 7 ASN A1063 PHE A1072 -1 O PHE A1069 N LEU A 872 SHEET 4 AA2 7 SER A 933 ASN A 943 -1 N ASN A 943 O ASN A1063 SHEET 5 AA2 7 PHE A1004 ASN A1011 -1 O ILE A1008 N ILE A 936 SHEET 6 AA2 7 ASN A1015 ILE A1020 -1 O TYR A1019 N THR A1007 SHEET 7 AA2 7 LYS A1023 LYS A1029 -1 O ILE A1025 N ILE A1018 SHEET 1 AA3 7 GLU A 888 GLU A 892 0 SHEET 2 AA3 7 LYS A 916 THR A 920 -1 O LYS A 916 N GLU A 892 SHEET 3 AA3 7 THR A1041 LYS A1048 -1 O ILE A1042 N VAL A 919 SHEET 4 AA3 7 TYR A 952 VAL A 958 -1 N THR A 953 O ASN A1047 SHEET 5 AA3 7 GLY A 963 ILE A 969 -1 O ILE A 966 N ILE A 955 SHEET 6 AA3 7 PHE A 972 LYS A 978 -1 O THR A 976 N SER A 965 SHEET 7 AA3 7 GLU A 984 SER A 990 -1 O GLN A 985 N LEU A 977 SHEET 1 AA413 VAL A1163 ILE A1170 0 SHEET 2 AA413 LYS A1173 MET A1179 -1 O TYR A1175 N THR A1168 SHEET 3 AA413 LEU A1190 LEU A1196 -1 O LEU A1196 N SER A1176 SHEET 4 AA413 HIS A1255 ILE A1264 -1 O ILE A1262 N VAL A1191 SHEET 5 AA413 ARG A1234 PHE A1245 -1 N SER A1239 O VAL A1261 SHEET 6 AA413 TYR A1220 SER A1227 -1 N LEU A1224 O LEU A1238 SHEET 7 AA413 VAL A1163 ILE A1170 0 SHEET 8 AA413 ILE A1144 ARG A1150 -1 N LYS A1147 O TYR A1165 SHEET 9 AA413 GLU A1107 ASN A1112 -1 N TYR A1108 O ILE A1144 SHEET 10 AA413 TRP A1278 PRO A1282 -1 O VAL A1281 N TYR A1109 SHEET 11 AA413 TYR A1220 SER A1227 -1 N SER A1222 O TRP A1278 SHEET 12 AA413 PHE A1209 ASN A1215 -1 N ILE A1210 O PHE A1225 SHEET 13 AA413 TYR A1220 SER A1227 -1 O PHE A1225 N ILE A1210 SHEET 1 AA5 2 ARG A1118 LYS A1123 0 SHEET 2 AA5 2 GLY A1126 THR A1131 -1 O VAL A1128 N SER A1121 SHEET 1 AA6 5 LEU B 879 ASP B 881 0 SHEET 2 AA6 5 LYS B 868 ASN B 874 -1 N GLN B 873 O MET B 880 SHEET 3 AA6 5 ASN B1063 PHE B1072 -1 O PHE B1069 N LEU B 872 SHEET 4 AA6 5 PHE B 905 GLY B 908 -1 N LEU B 907 O MET B1064 SHEET 5 AA6 5 GLN B 896 LEU B 897 -1 N GLN B 896 O LYS B 906 SHEET 1 AA7 7 LEU B 879 ASP B 881 0 SHEET 2 AA7 7 LYS B 868 ASN B 874 -1 N GLN B 873 O MET B 880 SHEET 3 AA7 7 ASN B1063 PHE B1072 -1 O PHE B1069 N LEU B 872 SHEET 4 AA7 7 SER B 933 ASN B 943 -1 N ASN B 943 O ASN B1063 SHEET 5 AA7 7 PHE B1004 ASN B1011 -1 O ILE B1008 N ILE B 936 SHEET 6 AA7 7 ASN B1015 ILE B1020 -1 O MET B1017 N THR B1009 SHEET 7 AA7 7 LYS B1023 LYS B1029 -1 O ILE B1025 N ILE B1018 SHEET 1 AA8 7 GLU B 888 GLU B 892 0 SHEET 2 AA8 7 LYS B 916 THR B 920 -1 O LYS B 916 N GLU B 892 SHEET 3 AA8 7 THR B1041 LYS B1048 -1 O ILE B1042 N VAL B 919 SHEET 4 AA8 7 TYR B 952 LYS B 959 -1 N THR B 953 O ASN B1047 SHEET 5 AA8 7 SER B 962 ILE B 969 -1 O ILE B 966 N ILE B 955 SHEET 6 AA8 7 PHE B 972 LYS B 978 -1 O THR B 976 N SER B 965 SHEET 7 AA8 7 GLU B 984 SER B 990 -1 O GLN B 985 N LEU B 977 SHEET 1 AA913 VAL B1163 ILE B1170 0 SHEET 2 AA913 LYS B1173 MET B1179 -1 O TYR B1175 N THR B1168 SHEET 3 AA913 LEU B1190 LEU B1196 -1 O GLY B1194 N GLY B1178 SHEET 4 AA913 HIS B1255 ILE B1264 -1 O ILE B1262 N VAL B1191 SHEET 5 AA913 ARG B1234 PHE B1245 -1 N SER B1239 O VAL B1261 SHEET 6 AA913 TYR B1220 SER B1227 -1 N LEU B1224 O LEU B1238 SHEET 7 AA913 VAL B1163 ILE B1170 0 SHEET 8 AA913 ILE B1144 ARG B1150 -1 N LYS B1147 O TYR B1165 SHEET 9 AA913 GLU B1107 ASN B1112 -1 N TYR B1108 O ILE B1144 SHEET 10 AA913 TRP B1278 PRO B1282 -1 O VAL B1279 N ILE B1111 SHEET 11 AA913 TYR B1220 SER B1227 -1 N SER B1222 O TRP B1278 SHEET 12 AA913 PHE B1209 ASN B1215 -1 N ILE B1210 O PHE B1225 SHEET 13 AA913 TYR B1220 SER B1227 -1 O PHE B1225 N ILE B1210 SHEET 1 AB1 2 ARG B1118 LYS B1123 0 SHEET 2 AB1 2 GLY B1126 THR B1131 -1 O VAL B1128 N SER B1121 LINK O3 NGA C 1 C1 GAL C 2 1555 1555 1.39 LINK O3 GAL C 2 C2 SIA C 3 1555 1555 1.48 LINK O3 NGA D 1 C1 GAL D 2 1555 1555 1.31 CISPEP 1 PHE A 901 PRO A 902 0 8.33 CISPEP 2 ASN A 943 LYS A 944 0 -4.12 CISPEP 3 PHE B 901 PRO B 902 0 4.53 CISPEP 4 ASN B 943 LYS B 944 0 -2.73 CRYST1 109.699 109.699 210.461 90.00 90.00 90.00 P 41 21 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009116 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004751 0.00000